Domain

A domain is a functional subunit of a protein.

Figure 1: Two domains in the human mutL homolog 1 protein, implicated in colon cancer, nonpolyposis type 2, are shown by NCBI's CDART program. The ATP-ase domain metabolizes ATP to release energy, and the DNA mismatch repair domain fixes errors in DNA during replication. The protein is 756 amino acids long, and the domains are in approximately the first 350 amino acids.

In principle, a domain is a discrete structural unit of a protein, capable of folding independently from the rest of the protein. However, domains can often be identified by non-structural approaches based on conserved amino acid sequences. For example, NCBI's Conserved Domain Database (CDD) uses information from curated multiple sequence alignments to idenitfy conserved sequence regions, or domains, in protein sequences.

Figure 2: Multiple sequence alignment showing conserved residues (amino acids) in the DNA mismatch repair domain. The aligned sequences are from various organisms, including human, Synechocystis sp. (a bacterium), mouse, fruit fly, Thermotoga maritima (a bacterium), Arabidopsis thaliana (a plant),Borrelia burgdorferi (a bacterium), and baker's yeast.

Sources:  figure 1 is taken from the NCBI CDART program, using the query sequence NP_000240 (756 amino acids long); figure 2 is taken from the NCBI CDD resource, showing an excerpt of the multiple sequence alignment used to identify the DNA mismatch repair domain (pfam01119.5); the definition was derived from the NCBI Field Guide Course Glossary